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A wrapper for running the Semi-Automated Metabolic Map Illustrator (SAMMI) using Python

Project description


This package provides a wrapper for running the Semi-Automated Metabolic Map Illustrator (SAMMI) from Python scripts and the Python command line. The SAMMI tool can be found at The package works with the COBRApy toolbox and requires an internet connection to render maps. For more complex, up-to-date examples and to learn how to use the tool please check out the examples in the Jupyter Notebook file.


The SAMMIpy documentation can be found here.


To install the package run pip install sammi from the Python command line.


To use the SAMMI package run import sammi from within your python code. The function sammi.plot reads the template file index.html located at sammi.__path__[0] + '\\browser', and outputs the generated map to the same folder in the file defined within the function (defaulting to index_load.html).

To open previously generated maps use sammi.openmap(htmlName). Once maps are generated they can be exported in the SAMMI specific format to be shared and saved.


For help check help(sammi.plot) within Python or read the SAMMIpy documentation here. Users can also look at the examples provided in the documentation and the Jupyter Notebook in this folder. All of the examples provided in the notebook can be run using sammi.test(n) where n ranges from zero to eleven.

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